bein

Bein is a workflow manager and miniature LIMS system built in the Bioinformatics and Biostatistics Core Facility of the EPFL. It fills the gap for the working scientist between the classical shell and big workflow managers like Galaxy and major LIMS systems like OpenBIS.

As a rough overview, Bein can help you if you

analyze lots of data, and the analyses share many common elements, but the analyses are sufficiently different that small tweaks and if statements in a single script will not suffice.

have from two to a hundred files that must analyzed in the same way, and you need to keep track of which results came from which file.

need to interleave computations with calls to external programs in your analyses.

If you have thousands of files to be analyzed in the same way, you would be better served by systems like Galaxy and OpenBIS. For running a couple, quick commands on a single file, the Unix shell remains the best tool. If you are running simulations, and are therefore not concerned with external programs or tracking lots of files, we recommend you look at Sumatra; but for many people, including most bioinformaticists, Bein hits a sweet spot.

Short facts

Supported by BBCF at EPFL - École Polytechnique Fédérale de Lausanne

Links

Bein Tutorial including the description how to install and set up bein